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In a surprising SEC filing released this afternoon, Facebook Inc (NASDAQ:FB) and Zynga Inc (NASDAQ:ZNGA) just made quite a few headlines. To give the short version of things(which this Business Insider author does quite nicely), both companies “have agreed to substantially change an agreement the two companies struck two years ago,” which had given “Zynga a privileged position on Facebook’s platform.”

The change now gives the social network the ability to develop games for its platform internally, effective March 31, 2013. While this is still months away, and we’re even further away from seeing any Facebook-ready games on the platform itself, the markets have responded rather abruptly, pushing shares of ZNGA down more than 10% to the $2.30 range.

Since the start of the week, shares of the troubled social gaming company had risen by more than 30 cents, though all of those gains are now erased. Facebook Inc (NASDAQ:FB)’s stock, meanwhile, has risen just a few bips in after-hours trading. Here’s a nice side-by-side comparison of how each company’s fortunes – at least in terms of market valuation – have diverged in recent months.

As you can clearly see, shares of FB have worked hard to make it back to ‘break-even,’ so to speak, over the past six months. Though Facebook is still down since late May, they still would’ve made a much better investment than – and one heck of a pairs trade with – Zynga. Since the start of the summer, Zynga has lost over half of its market value as a management shakeup and slowing revenues have had investors running for the exits.

As Bloomberg mentions, the decision to amend its agreement with Facebook Inc (NASDAQ:FB) is undoubtedly a piece of its “reorganization aimed at reviving growth by cutting costs and focusing on mobile,” which CRO Barry Cottle said would give his company “the flexibility to ensure the universal availability of our products and services.”

Though the decision to increase its independence while lessening its reliance on Facebook may be better for Zynga in the long run, investors haven’t had the chance to see exactly how Zynga plans to move forward on its own, thus the market’s bearish reaction is understandable. Let us know your thoughts on what this news may mean for both companies in the comments section below.